Search Results (52)

Generative artificial intelligence and foundation models have changed machine learning by allowing systems to produce readable text, realistic images, and other multimodal content with little direct input from a user. Foundation models are large neural networks trained on very large and varied datasets, and they form the core of many current generative AI (GenAI) systems. Their rapid development has led to major advances in areas like natural language processing, computer vision, multimodal learning, and robotics. Examples include GPT, LLaMA, and diffusion-based architectures, such as models often used for image generation. Systems such as Stable Diffusion show this shift by illustrating how AI can interpret information, draw basic inferences, and produce new outputs using more than one type of data. This review surveys common foundation model architectures and examines what they can do in generative tasks. It reviews Transformer, diffusion, and multimodal architectures, focusing on methods that support scaling and transfer across domains. The paper also reviews key approaches to pretraining and fine-tuning, including self-supervised learning, instruction tuning, and parameter-efficient adaptation, which support these systems’ ability to generalize across tasks. In addition to the technical details, this review discusses how GenAI is being used for text generation, image synthesis, robotics, and biomedical research. The study also notes continuing challenges, such as the high computing and energy demands of large models, ethical concerns about data bias and misinformation, and worries about privacy, reliability, and responsible use of AI in real settings. This review brings together ideas about model design, training methods, and social implications to point future research toward GenAI systems that are efficient, easy to interpret, and reliable, while supporting scientific progress and ethical responsibility. Full article

Scientific evidence is fundamental to uncovering insights about health, including food and nutritional claims. Substantiating such claims requires robust scientific procedures that often include clinical studies, biochemical analyses, and the examination of multiple forms of data. The growing capabilities of artificial intelligence (AI) and large language models (LLMs) present new opportunities for analyzing food–health relationships and supporting health claim validation. Yet, applying these technologies to the food and nutrition domain raises challenges that differ from those encountered in broader biomedical text mining (TM). In this perspective, we review key issues, including the complexity and heterogeneity of food-related data, the scarcity of food-specific language models and standardized resources, difficulties in interpreting nuanced and often contradictory evidence, and requirements for integrating AI tools into regulatory workflows. We compare modern LLM approaches with traditional TM methods and discuss how each may complement the other. Our position is that, despite their promise, current AI and LLM tools cannot yet reliably handle the subtleties of food–health evidence without substantial domain-specific refinement and human expert oversight. We advocate for hybrid approaches that combine the precision of established TM techniques with the analytical breadth of LLMs, supported by harmonized ontologies, multidimensional evaluation frameworks, and human-in-the-loop validation, particularly in regulatory contexts. We also highlight the importance of public education, transparent communication standards, and coordinated cross-disciplinary efforts to ensure these technologies serve broader goals of food safety, consumer trust, and global health. Full article

Advancements in natural language processing (NLP), particularly Large Language Models (LLMs), have greatly improved how we access knowledge. However, in critical domains like biomedicine, challenges like hallucinations—where language models generate information not grounded in data—can lead to dangerous misinformation. This paper presents a hybrid approach that combines LLMs with Knowledge Graphs (KGs) to improve the accuracy and reliability of question-answering systems in the biomedical field. Our method, implemented using the LangChain framework, includes a query-checking algorithm that checks and, where possible, corrects LLM-generated Cypher queries, which are then executed on the Knowledge Graph, grounding answers in the KG and reducing hallucinations in the evaluated cases. We evaluated several LLMs, including several GPT models and Llama 3.3:70b, on a custom benchmark dataset of 50 biomedical questions. GPT-4 Turbo achieved 90% query accuracy, outperforming most other models. We also evaluated prompt engineering, but found little statistically significant improvement compared to the standard prompt, except for Llama 3:70b, which improved with few-shot prompting. To enhance usability, we developed a web-based interface that allows users to input natural language queries, view generated and corrected Cypher queries, and inspect results for accuracy. This framework improves reliability and accessibility by accepting natural language questions and returning verifiable answers directly from the knowledge graph, enabling inspection and reproducibility. The source code for generating the results of this paper and for the user-interface can be found in our Git repository: https://git.zib.de/lpusch/cyphergenkg-gui, accessed on 1 November 2025. Full article

Herpesvirus infections, including herpes simplex virus (HSV), Epstein–Barr virus (EBV), and cytomegalovirus (CMV), present significant challenges in diagnosis, treatment, and transmission control. Despite advances in medical technology, managing these infections remains complex due to the viruses’ ability to establish latency and their widespread prevalence. Artificial Intelligence (AI) has emerged as a transformative tool in biomedical science, enhancing our ability to understand, predict, and manage infectious diseases. In veterinary virology, AI applications offer considerable potential for improving diagnostics, forecasting outbreaks, and implementing targeted control strategies. This review explores the growing role of AI in advancing our understanding of herpesvirus infection, particularly those caused by MDV, through improved detection, transmission modeling, treatment strategies, and predictive tools. Employing AI technologies such as machine learning (ML), deep learning (DL), and natural language processing (NLP), researchers have made significant progress in addressing diagnostic limitations, modeling transmission dynamics, and identifying potential therapeutics. Furthermore, AI holds the potential to revolutionize personalized medicine, predictive analytics, and vaccine development for herpesvirus-related diseases. The review concludes by discussing ethical considerations, implementation challenges, and future research directions necessary to fully integrate AI into clinical and veterinary practice. Full article

Retrieval-Augmented Generation (RAG) enhances large language models (LLMs) by integrating external knowledge retrieval to improve factual consistency and reduce hallucinations. Despite growing interest, its use in healthcare remains fragmented. This paper presents a Systematic Literature Review (SLR) following PRISMA guidelines, synthesizing 30 peer-reviewed studies on RAG in clinical domains, focusing on three of its most prevalent and promising applications in diagnostic support, electronic health record (EHR) summarization, and medical question answering. We synthesize the existing architectural variants (naïve, advanced, and modular) and examine their deployment across these applications. Persistent challenges are identified, including retrieval noise (irrelevant or low-quality retrieved information), domain shift (performance degradation when models are applied to data distributions different from their training set), generation latency, and limited explainability. Evaluation strategies are compared using both standard metrics and clinical-specific metrics, FactScore, RadGraph-F1, and MED-F1, which are particularly critical for ensuring factual accuracy, medical validity, and clinical relevance. This synthesis offers a domain-focused perspective to guide researchers, healthcare providers, and policymakers in developing reliable, interpretable, and clinically aligned AI systems, laying the groundwork for future innovation in RAG-based healthcare solutions. Full article

Purpose: Cancer immunotherapy has transformed oncology, but underserved populations face persistent disparities in access and outcomes. This review explores how artificial intelligence (AI) can help mitigate these barriers. Methods: We conducted a narrative review based on peer-reviewed literature selected for relevance to artificial intelligence, cancer immunotherapy, and healthcare challenges, without restrictions on publication date. We searched three major electronic databases: PubMed, IEEE Xplore, and arXiv, covering both biomedical and computational literature. The search included publications from January 2015 through April 2024 to capture contemporary developments in AI and cancer immunotherapy. Results: AI tools such as machine learning, natural language processing, and predictive analytics can enhance early detection, personalize treatment, and improve clinical trial representation for historically underrepresented populations. Additionally, AI-driven solutions can aid in managing side effects, expanding telehealth, and addressing social determinants of health (SDOH). However, algorithmic bias, privacy concerns, and data diversity remain major challenges. Conclusions: With intentional design and implementation, AI holds the potential to reduce disparities in cancer immunotherapy and promote more inclusive oncology care. Future efforts must focus on ethical deployment, inclusive data collection, and interdisciplinary collaboration. Full article

Despite remarkable advances in neural language models, a substantial gap remains in precisely interpreting the complex semantics of Electronic Medical Records (EMR). We propose Contrastive Representations Pre-Training (CRPT) to address this gap, replacing the conventional Next Sentence Prediction task’s cross-entropy loss with contrastive loss and incorporating whole-word masking to capture multi-token domain-specific terms better. We also introduce a carefully designed negative sampling strategy that balances intra-document and cross-document sentences, enhancing the model’s discriminative power. Implemented atop a BERT-based architecture and evaluated on the Biomedical Language Understanding Evaluation (BLUE) benchmark, our Discharge Summary CRPT model achieves significant performance gains, including a natural language inference precision of 0.825 and a sentence similarity score of 0.775. We further extend our approach through Bio+Discharge Summary CRPT, combining biomedical and clinical corpora to boost downstream performance across tasks. Our framework demonstrates robust interpretive capacity in clinical texts by emphasizing sentence-level semantics and domain-aware masking. These findings underscore CRPT’s potential for advancing semantic accuracy in healthcare applications and open new avenues for integrating larger negative sample sets, domain-specific masking techniques, and multi-task learning paradigms. Full article

This work introduces TrialSieve, a novel framework for biomedical information extraction that enhances clinical meta-analysis and drug repurposing. By extending traditional PICO (Patient, Intervention, Comparison, Outcome) methodologies, TrialSieve incorporates hierarchical, treatment group-based graphs, enabling more comprehensive and quantitative comparisons of clinical outcomes. TrialSieve was used to annotate 1609 PubMed abstracts, 170,557 annotations, and 52,638 final spans, incorporating 20 unique annotation categories that capture a diverse range of biomedical entities relevant to systematic reviews and meta-analyses. The performance (accuracy, precision, recall, F1-score) of four natural-language processing (NLP) models (BioLinkBERT, BioBERT, KRISSBERT, PubMedBERT) and the large language model (LLM), GPT-4o, was evaluated using the human-annotated TrialSieve dataset. BioLinkBERT had the best accuracy (0.875) and recall (0.679) for biomedical entity labeling, whereas PubMedBERT had the best precision (0.614) and F1-score (0.639). Error analysis showed that NLP models trained on noisy, human-annotated data can match or, in most cases, surpass human performance. This finding highlights the feasibility of fully automating biomedical information extraction, even when relying on imperfectly annotated datasets. An annotator user study (n = 39) revealed significant (p < 0.05) gains in efficiency and human annotation accuracy with the unique TrialSieve tree-based annotation approach. In summary, TrialSieve provides a foundation to improve automated biomedical information extraction for frontend clinical research. Full article

Background: Artificial Intelligence (AI) techniques, particularly Deep Learning (DL) and Natural Language Processing (NLP), have seen exponential growth in the biomedical field. This study focuses on enhancing predictive models for atrial fibrillation (AF) recurrence by extracting valuable data from electronic health records (EHRs) and unstructured medical reports. Although existing models show promise, their reliability is hampered by inaccuracies in coded data, with significant false positives and false negatives impacting their performance. To address this, the authors propose an automated system using DL and NLP techniques to process medical reports, extracting key predictive variables, and identifying new AF cases. The main purpose is to improve dataset reliability so future predictive models can respond more accurately Methods and Results: The study analyzed over one million discharge reports, applying regular expressions and DL tools to extract variables and identify AF onset. The performance of DL models, particularly a feedforward neural network combined with tf-idf, demonstrated high accuracy (0.986) in predicting AF onset. The application of DL tools on unstructured text reduced the error rate in AF identification by 50%, achieving an error rate of less than 2%. Conclusions: This work underscores the potential of AI in optimizing dataset accuracy to develop predictive models and consequently improving the healthcare predictions, offering valuable insights for research groups utilizing secondary data for predictive analytics in this particular setting. Full article

This research aims to investigate the roles of ontology and Semantic Web Technologies (SWT) in modern knowledge representation and data management. By analyzing a dataset of 10,037 academic articles from Web of Science (WoS) published in the last 6 years (2019–2024) across several fields, such as computer science, engineering, and telecommunications, our research identifies important trends in the use of ontologies and semantic frameworks. Through bibliometric and semantic analyses, Natural Language Processing (NLP), and topic modeling using Latent Dirichlet Allocation (LDA) and BERT-clustering approach, we map the evolution of semantic technologies, revealing core research themes such as ontology engineering, knowledge graphs, and linked data. Furthermore, we address existing research gaps, including challenges in the semantic web, dynamic ontology updates, and scalability in Big Data environments. By synthesizing insights from the literature, our research provides an overview of the current state of semantic web research and its prospects. With a 0.75 coherence score and perplexity = 48, the topic modeling analysis identifies three distinct thematic clusters: (1) Ontology-Driven Knowledge Representation and Intelligent Systems, which focuses on the use of ontologies for AI integration, machine interpretability, and structured knowledge representation; (2) Bioinformatics, Gene Expression and Biological Data Analysis, highlighting the role of ontologies and semantic frameworks in biomedical research, particularly in gene expression, protein interactions and biological network modeling; and (3) Advanced Bioinformatics, Systems Biology and Ethical-Legal Implications, addressing the intersection of biological data sciences with ethical, legal and regulatory challenges in emerging technologies. The clusters derived from BERT embeddings and clustering show thematic overlap with the LDA-derived topics but with some notable differences in emphasis and granularity. Our contributions extend beyond theoretical discussions, offering practical implications for enhancing data accessibility, semantic search, and automated knowledge discovery. Full article

The intense rising of machine learning in the previous years, bolstered by post-COVID-19 digitalization, left some of us pondering upon the transparency practices involving projects sourced from European Union funds. This study focuses on the European Union research clusters and trends in the ecosystem of higher education institutions (HEIs). The manually curated dataset of bibliometric data from 2020 to 2024 was analyzed in steps, from the traditional bibliometric indicators to natural language processing and collaboration networks. Centrality metrics, including degree, betweenness, closeness, and eigenvector centrality, and a three-way-intersection of community detection algorithms were computed to quantify the influence and the connectivity of institutions in different communities in the collaborative research networks. In the EU context, results indicate that institutions such as Universidad Politecnica de Madrid, the University of Cordoba, and Maastricht University frequently occupy central positions, echoing their role as local or regional hubs. At the global level, prominent North American and UK-based universities (e.g., University of Pennsylvania, Columbia University, Imperial College London) also remain influential, standing as a witness to their enduring influence in transcontinental research. Clustering outputs further confirmed that biomedical and engineering-oriented lines of inquiry often dominated these networks. While multiple mid-ranked institutions do appear at the periphery, the data highly implies that large-scale initiatives gravitate toward well-established players. Although the recognized centers provide specialized expertise and resources, smaller universities typically rely on a limited number of niche alliances. Full article

Ontologies are critical for organizing and interpreting complex domain-specific knowledge, with applications in data integration, functional prediction, and knowledge discovery. As the manual curation of ontology annotations becomes increasingly infeasible due to the exponential growth of biomedical and genomic data, natural language processing (NLP)-based systems have emerged as scalable alternatives. Evaluating these systems requires robust semantic similarity metrics that account for hierarchical and partially correct relationships often present in ontology annotations. This study explores the integration of graph-based and language-based embeddings to enhance the performance of semantic similarity metrics. Combining embeddings generated via Node2Vec and large language models (LLMs) with traditional semantic similarity metrics, we demonstrate that hybrid approaches effectively capture both structural and semantic relationships within ontologies. Our results show that combined similarity metrics outperform individual metrics, achieving high accuracy in distinguishing child–parent pairs from random pairs. This work underscores the importance of robust semantic similarity metrics for evaluating and optimizing NLP-based ontology annotation systems. Future research should explore the real-time integration of these metrics and advanced neural architectures to further enhance scalability and accuracy, advancing ontology-driven analyses in biomedical research and beyond. Full article

Named Entity Recognition (NER) is a fundamental task in Natural Language Processing (NLP) that supports applications such as information retrieval, sentiment analysis, and text summarization. While substantial progress has been made in NER for widely studied languages like English, Arabic presents unique challenges due to its morphological richness, orthographic ambiguity, and the frequent occurrence of nested and overlapping entities. This paper introduces a novel Arabic NER framework that addresses these complexities through architectural innovations. The proposed model incorporates a Hybrid Feature Fusion Layer, which integrates external lexical features using a cross-attention mechanism and a Gated Lexical Unit (GLU) to filter noise, while a Compound Span Representation Layer employs Rotary Positional Encoding (RoPE) and Bidirectional GRUs to enhance the detection of complex entity structures. Additionally, an Enhanced Multi-Label Classification Layer improves the disambiguation of overlapping spans and assigns multiple entity types where applicable. The model is evaluated on three benchmark datasets—ANERcorp, ACE 2005, and a custom biomedical dataset—achieving an F1-score of 93.0% on ANERcorp and 89.6% on ACE 2005, significantly outperforming state-of-the-art methods. A case study further highlights the model’s real-world applicability in handling compound and nested entities with high confidence. By establishing a new benchmark for Arabic NER, this work provides a robust foundation for advancing NLP research in morphologically rich languages. Full article

The extraction of Adverse Drug Reactions from biomedical text is a critical task in the field of healthcare and pharmacovigilance. It serves as a cornerstone for improving patient safety by enabling the early identification and mitigation of potential risks associated with pharmaceutical treatments. This process not only helps in detecting harmful side effects that may not have been evident during clinical trials but also contributes to the broader understanding of drug safety in real-world settings, ultimately guiding regulatory actions and informing clinical practices. In this study, we conducted a comprehensive evaluation of eleven transformer-based models for ADR extraction, focusing on two widely used datasets: CADEC and SMM4H. The task was approached as a sequence labeling problem, where each token in the text is classified as part of an ADR or not. Various transformer architectures, including BioBERT, PubMedBERT, and SpanBERT, were fine-tuned and evaluated on these datasets. BioBERT demonstrated superior performance on the CADEC dataset, achieving an impressive F1 score of 86.13%, indicating its strong capability in recognizing ADRs within patient narratives. On the other hand, SpanBERT emerged as the top performer on the SMM4H dataset, with an F1 score of 84.29%, showcasing its effectiveness in processing the more diverse and challenging social media data. These results highlight the importance of selecting appropriate models based on the specific characteristics such as text formality, domain-specific language, and task complexity to achieve optimal ADR extraction performance. Full article

In the expanding landscape of biomedical literature, numerous latent associations outlined in scholarly papers await discovery and integration into biomedical databases. Biomedical Natural Language Processing (NLP) research focuses on automating knowledge extraction and mining from this literature, particularly emphasizing the essential task of Relation Extraction (RE). However, existing models have limitations, mainly in their applicability to partial datasets for RE tasks. Moreover, conventional models often treat RE as a binary classification challenge, which proves suboptimal given the diverse relationships, including intricate ones like similarity and hierarchy, present in the RE dataset. These limitations are exacerbated by the models’ inability to capture word-level positional nuances and sentence-level language features. In response to these challenges, we present a novel RE model called BicapBert. This model integrates neural networks and capsule networks, enhancing them with hybrid knowledge graph embeddings to extract relevant features. BicapBert utilizes PubMedBERT and capsule networks to extract word-level positional and sentence-level language features. It further captures knowledge features from a biomedical knowledge graph, integrating them with the aforementioned linguistic features. The amalgamated information is then input into a multi-layer perceptron, culminating in results derived through a softmax classifier. Experimental evaluations on three extensive RE task datasets showcase the state-of-the-art performance of our proposed model. Additionally, we validate the model’s efficacy on three randomly selected biomedical datasets for various tasks, further affirming its superiority. Full article